Looking at your screen output your pakfire update command has downloaded the lists. The size is listed against each of the downloads and those sizes are around what would be expected.
Then your pakfire status command says that it can’t find the core-list.db file that was just downloaded.
It also looks like none of those files have been able to be saved into that directory as the age of all three files has been taken as 20502d 12h 56m 34s and that is basically as the files don’t exist it has taken the start of the Linux Epoch (1/1/1970 00:00:00) as the date of the files.
The update command first downloads those db files into a cache dir and does various checks and then if those are okay it then transfers them to the lists directory.
If you run the command ls -hal /opt/pakfire/db/lists does that show the directory being empty?
Do you find any of the .db files in /var/cache/pakfire/
When I want to restore damaged, deleted, or incorrectly modified files, I download the corresponding IPFire ISO and extract it with 7-Zip until the file system is extracted. Then, using WinSCP, I upload them to the correct location.
Of course, I have to correctly apply the user/group permissions.
Then that is your problem. Somehow you have deleted the directory.
You have ended up with core-list.db in the /opt/pakfire/db directory. That must also have been manually done as the code will only try and place it in the lists directory and not in the db directory.
Also the directories labelled core, installed, meta and rootfiles are also missing.
As it might not be certain what other changes/errors there are elsewhere, my suggestion would be to do a backup and download it off of your IPFire system. Then do a fresh install using CU199 and then do a restore from the backup.